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| Status |
Public on May 31, 2018 |
| Title |
sch9wild_wk02_af107 |
| Sample type |
SRA |
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| Source name |
Human embryonic stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
time point: week 2
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| Treatment protocol |
GSE106245
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| Growth protocol |
The Eiraku et al., 2008 cortical organoid differentiation protocol was used with modifications. Human embryonic stem cells were grown in feeder-free conditions on vitronectin (ThermoFisher) with Essential-8 Flex media (ThermoFisher) and 10,000 cells per EB were aggregated using AggreWell-800 plates (Stem Cell Technologies) in Aggrewell media (Stem Cell Technologies) supplemented with 10 uM Y-27632 rock inhibitor (ATCC) and transferred to low attachment plates (Corning) on day 2. Media was supplemented with 500ng/mL DKK1 (Peprotech), 500 ng/mL NOGGIN (R & D Systemes), 10 uM SB431542 (Sigma), and 1 uM Cyclopamine V. californicum (VWR) for the first 18 days of differentiation. The media was changed to Neuralbasal (Invitrogen) supplemented with N2 (Gibco) and 1 uM Cyclopamine on day 18. Neurospheres were supplemented with 10ng/mL bFGF and 10ng/mL EGF to improve survivability in Neuralbasal media. After day 26, the media was switched to Neuralbasal/N2 media without any added factors.
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| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Chromium single cell RNA-seq RevA and RevB as indicated
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
10X RevB pipeline
single cell RNA
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| Data processing |
The "cellranger mkref" command was used with the (hg19) FANTOM lv3 (Hon et al, 2017) gene model to createthe reference used by "cellranger count" to align the reads and assign them to genes
The 10X supplied cellranger software version 2.0.0 was used. The "cellranger count" command was used with default parameters (and --expect-cells=3000), with the genome target of hg19 and a gene model derived from FANTOM
Genome_build: hg19, FANTOM lv3 (Hon et al, 2017) transcripts
Supplementary_files_format_and_content: gene-by-cell matrixin MatrixMarket format
Supplementary_files_format_and_content: barcodes.tsv genes.tsv matrix.mtx
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| Submission date |
Nov 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Ryan Field |
| E-mail(s) |
andrew_field@hms.harvard.edu
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| Organization name |
Harvard Medical School
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| Department |
BCMP
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| Lab |
Adelman
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| Street address |
45 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE106245 |
Human embryonic stem cell, chimpanzee induced pluripotent stem cell, orangutan induced pluripotent stem cell, rhesus embryonic stem cell, and their derived cortical organoid RNA-seq |
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| Relations |
| BioSample |
SAMN08108174 |
| SRA |
SRX3428257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2867934_sch9wild_wk02_af107_filtered_gene_bc_matrix.tar.gz |
21.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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